Aftermath: Some Assembly Required
by LiveAndLetRain
Summary: Tony Stark had plans after the disaster with Extremis. Plans that included Pepper and Stark Industries. And most definitely did not include the other "Avengers." And then SHIELD blew up. Overlaps with and is a sequel to "Silver Arrow."
1. In Which Tony Watches The News

**I do not own the Avengers.**

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Tony was in the middle of replacing the last of You's inner workings when JARVIS spoke up.

"Sir. I believe you should join Miss Potts in the sitting room. She is distressed."

That got his attention. "Why?" He didn't wait for JARVIS to answer before dashing off towards the elevator, leaving the newly restored Dummy and Butterfingers beeping worriedly behind him as he left the lab.

"It is the news, Sir." JARVIS explained as he helpfully sent the elevator upwards at near top speed. (Pepper had forbidden top speed. It tended to leave the occupant flattened on the floor.) "Something appears to be occurring in Washington D.C. It involves S.H.I.E.L.D., Captain Rogers, and Agent Romanoff."

Tony swore and burst out of the elevator almost before JARVIS opened the door. Pepper had been spending the day overseeing the coating of the Loki-hole in the living room with gold alloy. If whatever was going down was bad enough to have her retreating to the sitting room…For a moment, Tony felt extremely vulnerable. He reminded himself firmly that he had given up the Iron Man gig and managed to grind to a halt before he ran Pepper over.

She was standing in the middle of the room, tears running down her face, watching the figures moving on the StarkScreen in front of the wall. Tony turned to look.

The screen was covered with images of Red and some other guy being pushed into an armored truck, and Capsicle kneeling on the pavement, surrounded by smoking, ruined cars, his shield lying beside him, and _a freaking gun pointed at his head!_

The truck has the S.H.E.I.L.D. logo on it. The guy standing behind Cap glanced up, straight at the camera, and looked back down. The guy pointing the gun stepped back and they manhandled Rogers to his feet and into the truck.

The entire scene was no longer than ten seconds.

Tony was still frozen in shock when JARVIS spoke again. "Sir. There is something else I believe you should know."

Tony felt his mouth work for several seconds before sound came out. "What."

"Director Fury is dead Sir. As of 1:03 AM yesterday."

"WHAT!" He inadvertently knocked Pepper's arm aside as he began to frantically pace with short, sharp steps. "Why are we only finding out about this now?"

"Because Sir," JARVIS explained in his rational tone with just a hint of sarcasm that was totally not in the programming Tony put into him. "System reboot began two days ago at noon."

Tony groaned and smacked his hand against his face rather harder than he should have. "Of course," he muttered, still pacing. "We turn you off for thirty-seven point four hours and the world goes to hell in a handbasket."

He turned and looked at Pepper, not sure how to say the words hovering just behind his lips. She smiled sadly at him. "I know you have the materials to make a new suit Tony." She said quietly. "Go on."

The next twenty-four hours were a flurry of frantic activity as Tony began assembling a new suit, trying desperately not to think if Cap and Red had really gone off the deep end, (Though the probabilities are about 56% in favor of it being S.H.I.E.L.D. that's lost it) and JARVIS attempted to get into S.H.I.E.L.D.'s systems to figure out what is going on, only to be blocked out by some program that JARVIS reports (sounding incredibly disturbed) "It seems to be_…sentient_ Sir."

Tony left the suit to the bots and joined JARVIS.

And so the two of them had a front row seat when all of S.H.I.E.L.D.'s secrets were dumped onto the internet, and suddenly H.Y.D.R.A. was no longer just the stuff of nightmares and bad memories from decades gone by.

Tony sat in shock for approximately a tenth of a second before jumping into action.

"JARVIS! Isolate all information about Fury, the Avengers, SI, Agent Agent, and anyone else we care about. We need to filter this."

"At once Sir." JARVIS said. "Parameters?"

Tony thought a moment as he swept his hands across the projected StarkScreen. "We can't just delete it all unfortunately, that would look extremely suspicious. We need to edit. Anything they have on Pepper outside of the most bare-bones business file. Any and all information that could lead to connections between Dr. Banner and The Hulk. The locations of Thor and his girlfriend, as well as their relationship and connection. As much as possible about Cap, personal stuff. The Wonder-Twins too. Don't bother with the general stuff, but if you find anything that seems personal to them, hide it. Fury and Hill…Use your own judgment."

"And Agent Coulson, Sir?"

Tony swallowed against the lump in his throat. "Anything. His very existence. Those vultures don't need to get their hands on him."

"Acknowledged Sir." The tinge of grief in JARVIS' voice was almost too much for Tony.

"Tony?"He turned, Pepper was standing in the door of the lab, looking shell-shocked.

Then the lights flickered.

This was Stark Tower. The lights don't "flicker".

"JARVIS." Tony said cautiously. "Security report?"

"There seem to be several armed intruders three floors down, Sir." JARVIS reported serenely.

Tony's eyes widened. "How long until you can finish the suit?"

"Approximately seventy-one seconds, Sir."

Tony nodded. "Pepper, get to the safe room."

Pepper didn't argue, (he loves that woman so much) knowing that now was not the time to go through their usual routine. She vanished down the hall towards the sitting room, headed for the hidden elevator that would take her to the sub-level of the basement that was set up to stop everything up to and including a nuclear blast.

Fifty-nine seconds.

Once she was safely in the elevator, Tony locked down the lab. Lights off, doors closed, glass bullet-proofed. The only movement coming from the mechanical arms JARVIS utilized to put the final touches on the Suit, even the bots had retreated and were huddled in corners and under tables.

Thirty-seven seconds.

A dark figure moved on the other side of the glass. Tony crouched behind a table, shushing Butterfingers on the way down and slipping on the control bracelets for the suit. Automatically, his hand went to his chest, searching for the familiar sensation of the arc-reactor.

_Oh, right, surgery. Not there anymore. The new suit has a built in reactor. _

Thirty-one seconds.

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_**There are nine more chapters to come!**_

_**Please review, Bob is loosing weight at a horrible rate. I'm worried about him.**_


	2. In Which They Have An Agent

The irony of it all was that Tony needn't really have bothered. It was rather sad actually, whatever woefully underprepared morons H.Y.D.R.A.S.H.I.E.L.D. had sent after him had turned a missile launcher onto the windows of the lab. The windows that were made of a specially designed, multi-layered, fiber-glass and highly-classified-materials blend that Tony himself had developed with the express purpose of keeping _Pepper_ safe. Though to be fair, even he wasn't exactly expecting the missile to _bounce._ That had never happened in testing, must be old Hammer Tech.

After that it was simply a matter of waiting the remaining sixteen seconds for J.A.R.V.I.S. and the 'bots to finish the suit, suiting up, and strolling out into the corridor to punch the two who hadn't been taken out by their own stupidity and high explosives. It was really rather anti-climactic. The hard part was what to do with them afterwards, he couldn't exactly call S.H.I.E.L.D. in to haul them off.

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It took a while, what with all the drama going on in D.C., but they were eventually able to hand off the surviving Hydroids, (No Pepper, that is a totally awesome name, it isn't stupid) to Rhodey and a bunch of National Guard he brought with him, barreling in to the rescue at top speeds only to find Tony, Pepper, Happy, and the 'bots standing guard over a handful of dazed and unconscious would-be killers. (And carefully ignoring the still-smoking, self-caused corpses of the others.)

Apparently it had all worked out, sorta, because Stalin and Cap had lead a coup of some sort and managed to defeat H.Y.D.R.A., something the tower's invaders must not have been aware of. The more he learned of the situation, the plainer it became the minions that had been sent after him and Pep were what were left _after_ the bottom of the barrel had been scraped. It was mildly insulting.

Of course, then he found out about the D.N.A. targeting system being calibrated to take out a long list of people that he _knew_ included himself and, more importantly, Pepper. No one ever confirmed that, but they didn't need to.

See if he ever let anyone have any of his tech ever again. People couldn't be trusted.

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After that, things actually came around to something resembling normal, Romanoff was busy on Capitol Hill being called to the stand for S.H.I.E.L.D's accountability (or lack thereof) and Cap and his new friend (Sam Wilson, formerly of the U.S. Air Force, Operation: Falcon, worked with the VA as a shrink-like person) seemed to have disappeared.

The media hadn't calmed down much, but there were beginning to be headlines about other things besides the evil terrorist organization bound and determined to take over the world from its hiding place within the world's most shadowiest shadow agency. Spiderman was back in the news other than just _The Bugle_ anyway. He'd been in and out of the spotlight since his first appearances in June and July of 2012. Tony was positive he saw him once, but Pepper and Happy are both skeptical. There were rumors of vigilantes in the various locals of New York City, mostly in and around Hell's Kitchen, which had been knocked back into it's historical status of un-gentrification by the various attacks that happened in the vicinity. Some nutjob blew up what turned out to have been a H.Y.D.R.A. outpost near Phoenix, AZ of all places.

The uptick in freelancer "justice" had Tony rather worried. It seemed like these days anyone one could put on a mask and get away with murder. He was distinctly reminded of his speech, what seemed like a life-time ago. "A system that is comfortable with zero accountability." Had no one learned from the H.Y.D.R.A.S.H.I.E.L.D debacle that had only just happened, mere days ago?

He was…considering (not brooding) the subject when he decided that he missed Pepper and wandered out of his lab and towards her office. She wasn't there and her secretary (Amy? Andrea? Angela?) said she had gone down to meet with the director of HR. After a consultation with JARVIS that revealed HR's location to be on the sixth and seventh floors, Tony got back into the elevator and headed down.

He didn't bother knocking, and strode right into the Director's office. "Hey Pep, so I was thinking-" He stopped so suddenly that he almost ran into the chair Pepper was sitting in. "What is she doing here?"

Maria Hill was sitting on the far side of the desk, looking prim and proper and as if there was nothing whatsoever wrong with her being _here_ in _Tony's_ building. "What is she doing here? Get rid of her."

Pepper has her _Tony-be-reasonable_ look on. "Maria has been working with us to sort out people we can and can't trust."

Tony just looks at them both, feeling pricks of pain where his ragged fingernails are digging into his palms. "That would be nice." he says and doesn't even feel ashamed of the bitterness in his voice. "If we, you know, knew we can trust _her."_

Hill doesn't even have the decency to look insulted, just shuffles around the stack of papers on her desk. (And why are there _papers_ in Tony's tech-age tower?)

"You might not like it Stark, but with the destruction of S.H.I.E.L.D as we knew it there is a void in the protection of this world. Stark Industries is most qualified to assist in repairing that void. I am here because no one else was available and willing."

Pepper doesn't actually look all that happy with the situation herself, but she is nodding along. "She came to me Tony. She was honest about what she wanted and what she could give."

"What do you want?" Tony asked sarcastically, arms folded across his chest to protect an arc reactor that is no longer there. "What can we do for the high and mighty fallen S.H.I.E.L.D.?"

"You can reform the Avengers."

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**Please review?**

_**Also, I apologize for the long wait. Updates should be fairly regular from here on out.**_


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